2yor: Difference between revisions

Revision as of 13:00, 22 July 2020

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

Structural highlights

2yor is a 2 chain structure with sequence from Agrocybe aegerita. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	BMA, CL, HEM, MAN, MG, MZ0, NAG, SO4, TRS
Related:	2yp1
Activity:	Unspecific peroxygenase, with EC number 1.11.2.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[APO1_AGRAE] Aromatic peroxidase that oxidizes aryl alcohols into the corresponding aldehydes and then into the corresponding benzoic acids. Oxidizes toluene and naphthalene. Catalyzes the regioselective peroxide-dependent hydroxylation of propranolol and diclofenac to 5-hydroxypropranolol and 4'-hydroxydiclofenac. Catalyzes the regioselective peroxide-dependent hydroxylation of naphthalene to 1-naphthol or 2-naphthol via a naphthalene 1,2-oxide intermediate. Catalyzes the regioselective peroxide-dependent oxidation of pyridine to pyridine N-oxide. Halogenates monochlorodimedone and phenol. Oxidizes the sulfer-containing heterocycle dibenzothiophene to yield ring-hydroxylation products and to a lesser extent sulfoxidation products.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio and stereoselectivities. Compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand-binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons (PAHs). Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO.

Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits.,Piontek K, Strittmatter E, Ullrich R, Grobe G, Pecyna MJ, Kluge M, Scheibner K, Hofrichter M, Plattner DA J Biol Chem. 2013 Oct 14. PMID:24126915^[8]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ullrich R, Nuske J, Scheibner K, Spantzel J, Hofrichter M. Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Appl Environ Microbiol. 2004 Aug;70(8):4575-81. PMID:15294788 doi:https://dx.doi.org/10.1128/AEM.70.8.4575-4581.2004
↑ Ullrich R, Hofrichter M. The haloperoxidase of the agaric fungus Agrocybe aegerita hydroxylates toluene and naphthalene. FEBS Lett. 2005 Nov 7;579(27):6247-50. Epub 2005 Oct 19. PMID:16253244 doi:https://dx.doi.org/10.1016/j.febslet.2005.10.014
↑ Kluge MG, Ullrich R, Scheibner K, Hofrichter M. Spectrophotometric assay for detection of aromatic hydroxylation catalyzed by fungal haloperoxidase-peroxygenase. Appl Microbiol Biotechnol. 2007 Jul;75(6):1473-8. Epub 2007 Apr 5. PMID:17410351 doi:https://dx.doi.org/10.1007/s00253-007-0942-8
↑ Ullrich R, Dolge C, Kluge M, Hofrichter M. Pyridine as novel substrate for regioselective oxygenation with aromatic peroxygenase from Agrocybe aegerita. FEBS Lett. 2008 Dec 10;582(29):4100-6. doi: 10.1016/j.febslet.2008.11.006. Epub, 2008 Nov 18. PMID:19022254 doi:https://dx.doi.org/10.1016/j.febslet.2008.11.006
↑ Aranda E, Kinne M, Kluge M, Ullrich R, Hofrichter M. Conversion of dibenzothiophene by the mushrooms Agrocybe aegerita and Coprinellus radians and their extracellular peroxygenases. Appl Microbiol Biotechnol. 2009 Apr;82(6):1057-66. doi:, 10.1007/s00253-008-1778-6. Epub 2008 Nov 28. PMID:19039585 doi:https://dx.doi.org/10.1007/s00253-008-1778-6
↑ Kluge M, Ullrich R, Dolge C, Scheibner K, Hofrichter M. Hydroxylation of naphthalene by aromatic peroxygenase from Agrocybe aegerita proceeds via oxygen transfer from H2O2 and intermediary epoxidation. Appl Microbiol Biotechnol. 2009 Jan;81(6):1071-6. doi: 10.1007/s00253-008-1704-y., Epub 2008 Sep 25. PMID:18815784 doi:https://dx.doi.org/10.1007/s00253-008-1704-y
↑ Kinne M, Poraj-Kobielska M, Aranda E, Ullrich R, Hammel KE, Scheibner K, Hofrichter M. Regioselective preparation of 5-hydroxypropranolol and 4'-hydroxydiclofenac with a fungal peroxygenase. Bioorg Med Chem Lett. 2009 Jun 1;19(11):3085-7. doi: 10.1016/j.bmcl.2009.04.015. , Epub 2009 Apr 9. PMID:19394224 doi:https://dx.doi.org/10.1016/j.bmcl.2009.04.015
↑ Piontek K, Strittmatter E, Ullrich R, Grobe G, Pecyna MJ, Kluge M, Scheibner K, Hofrichter M, Plattner DA. Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits. J Biol Chem. 2013 Oct 14. PMID:24126915 doi:https://dx.doi.org/10.1074/jbc.M113.514521

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OCA

[1] Ullrich R, Nuske J, Scheibner K, Spantzel J, Hofrichter M. Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Appl Environ Microbiol. 2004 Aug;70(8):4575-81. PMID:15294788 doi:https://dx.doi.org/10.1128/AEM.70.8.4575-4581.2004

[2] Ullrich R, Hofrichter M. The haloperoxidase of the agaric fungus Agrocybe aegerita hydroxylates toluene and naphthalene. FEBS Lett. 2005 Nov 7;579(27):6247-50. Epub 2005 Oct 19. PMID:16253244 doi:https://dx.doi.org/10.1016/j.febslet.2005.10.014

[3] Kluge MG, Ullrich R, Scheibner K, Hofrichter M. Spectrophotometric assay for detection of aromatic hydroxylation catalyzed by fungal haloperoxidase-peroxygenase. Appl Microbiol Biotechnol. 2007 Jul;75(6):1473-8. Epub 2007 Apr 5. PMID:17410351 doi:https://dx.doi.org/10.1007/s00253-007-0942-8

[4] Ullrich R, Dolge C, Kluge M, Hofrichter M. Pyridine as novel substrate for regioselective oxygenation with aromatic peroxygenase from Agrocybe aegerita. FEBS Lett. 2008 Dec 10;582(29):4100-6. doi: 10.1016/j.febslet.2008.11.006. Epub, 2008 Nov 18. PMID:19022254 doi:https://dx.doi.org/10.1016/j.febslet.2008.11.006

[5] Aranda E, Kinne M, Kluge M, Ullrich R, Hofrichter M. Conversion of dibenzothiophene by the mushrooms Agrocybe aegerita and Coprinellus radians and their extracellular peroxygenases. Appl Microbiol Biotechnol. 2009 Apr;82(6):1057-66. doi:, 10.1007/s00253-008-1778-6. Epub 2008 Nov 28. PMID:19039585 doi:https://dx.doi.org/10.1007/s00253-008-1778-6

[6] Kluge M, Ullrich R, Dolge C, Scheibner K, Hofrichter M. Hydroxylation of naphthalene by aromatic peroxygenase from Agrocybe aegerita proceeds via oxygen transfer from H2O2 and intermediary epoxidation. Appl Microbiol Biotechnol. 2009 Jan;81(6):1071-6. doi: 10.1007/s00253-008-1704-y., Epub 2008 Sep 25. PMID:18815784 doi:https://dx.doi.org/10.1007/s00253-008-1704-y

[7] Kinne M, Poraj-Kobielska M, Aranda E, Ullrich R, Hammel KE, Scheibner K, Hofrichter M. Regioselective preparation of 5-hydroxypropranolol and 4'-hydroxydiclofenac with a fungal peroxygenase. Bioorg Med Chem Lett. 2009 Jun 1;19(11):3085-7. doi: 10.1016/j.bmcl.2009.04.015. , Epub 2009 Apr 9. PMID:19394224 doi:https://dx.doi.org/10.1016/j.bmcl.2009.04.015

[8] Piontek K, Strittmatter E, Ullrich R, Grobe G, Pecyna MJ, Kluge M, Scheibner K, Hofrichter M, Plattner DA. Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits. J Biol Chem. 2013 Oct 14. PMID:24126915 doi:https://dx.doi.org/10.1074/jbc.M113.514521

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[2]

[3]

[4]

[5]

[6]

[7]

[8]

@@ Line 1: / Line 1: @@
 ==Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron==
-<StructureSection load='2yor' size='340' side='right' caption='[[2yor]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
+<StructureSection load='2yor' size='340' side='right'caption='[[2yor]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yor]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrocybe_aegerita Agrocybe aegerita]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YOR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YOR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yor]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrocybe_aegerita Agrocybe aegerita]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YOR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2YOR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MZ0:1H-IMIDAZOL-5-YLMETHANOL'>MZ0</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MZ0:1H-IMIDAZOL-5-YLMETHANOL'>MZ0</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2yp1|2yp1]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_peroxygenase Unspecific peroxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.2.1 1.11.2.1] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yor OCA], [http://pdbe.org/2yor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yor RCSB], [http://www.ebi.ac.uk/pdbsum/2yor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yor ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2yor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yor OCA], [http://pdbe.org/2yor PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yor RCSB], [http://www.ebi.ac.uk/pdbsum/2yor PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yor ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 25: / Line 25: @@
 </StructureSection>
 [[Category: Agrocybe aegerita]]
+[[Category: Large Structures]]
 [[Category: Unspecific peroxygenase]]
 [[Category: Hofrichter, M]]

2yor: Difference between revisions

Revision as of 13:00, 22 July 2020

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

Structural highlights

Function

Publication Abstract from PubMed

References

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